Running and Verifying Bowtie2

Procedure

1. Use PuTTY to log in to the server as the root user.
2. Run the following command to run Bowtie2 and obtain the SAM file:

   bowtie2 -p 6 -3 5 --local -x mm10 -1 bowtie2-2.4.1/example/reads/reads_1.fq -2 bowtie2-2.4.1/example/reads/reads_2.fq -S example.sam

   The following is an example of the test result.

   10000 reads; of these: 
   10000 (100.00%) were paired; of these:
   10000 (100.00%) aligned concordantly 0 times
   0 (0.00%) aligned concordantly exactly 1 time 
   0 (0.00%) aligned concordantly >1 times 
   0.00% overall alignment rate